Pertronix Ignition problems

I have a 1966 Mustang 289 and have been working on getting the Pertronix Ignitor II to work in it. I have purchased the ignition, flamethrower 2 coil, and a new set of flamethrower spark plug wires. The car doesnt run very well anymore with the points (it doesnt fire every time) so I decided to upgrade it. I am pretty sure I have installed everything as the instructions say but, the car never starts. I have the ignitor gaped to .030" and have all my spark plug wires in correct order. What are some common mistakes that people make when installing these? Any response is greatly appreciated! Thanks